Tax withholding does not specifically apply to any particular portion of your tax liability, it is credited against your overall tax liability. It just so happens that the default tax withholding on an IRA distribution is the same percentage that Congress chose as the percentage excise tax on an early distribution, but that doesn't mean that the 10% withheld for taxes is the early-distribution penalty.
Once the IRS has the money that was withheld for taxes, the only way to get back anything is to file a tax return showing that your overall tax liability for the year is less than the amount that you paid the IRS in tax withholding and estimated taxes. The reason that your tax liability was less than the amount paid in tax withholding and estimated taxes is irrelevant.
